Reconstructing the History of Lineages
Chapter 11
Tereza JezkovaSchool of Life Sciences,
University of Nevada, Las Vegas
March 2011
study of evolutionary relatedness among organisms (through molecular data and morphological data)
PHYLOGENETICS
Cladograms
ABCDEOtaxon
Common Ancestor
Sister taxa
THE basic logic of phylogenetics:a natural taxon is a monophyletic group(all descendant taxa and their common ancestor)
ABCDEO
Common Ancestor
monophyletic
Common Ancestor
monophyletic
Fig. 11.4A
THE basic logic of phylogenetic systematics:a natural taxon is a monophyletic group(all descendant taxa and their common ancestor)
ABCDEO
Fig. 11.4A
ABCDEO
Other kinds of groups are not natural:paraphyletic groups (some, but not all
descendant taxa and their common ancestor)
Fig. 11.4B
Example of a paraphyletic group: Reptiles are paraphyletic if birds are removed
Other kinds of groups are not natural:polyphyletic groups (descendant taxa trace back
through two or more ancestors before reaching a common ancestor)
Fig. 11.4C
ABCDEO
Example of a polyphyletic group: warm-blooded animals (Mammals+Birds)
Characters (morphological, ecological, behavioral, molecular): traits that vary across taxa and clades
primitive character state
derived character state
character state change
homologous characters (homology): characters whose traits are shared between two
or more taxa or clades because of inheritance from a common ancestor
homologous characters (homology): characters whose traits are shared between two
or more taxa or clades because of inheritance from a common ancestor
pouch
pouchpouch
KOALA
POSSUM
homoplasious characters (homoplasy): characters whose traits are shared between two
or more taxa but evolved independently
homoplasious characters (homoplasy): characters whose traits are shared between two
or more taxa but evolved independently
FINS
FINS
FINSFINS
NOT USEFUL
character state evolution
primitive character state
derived character state
character state change
characters:
Primitive character state is not to have feathers
birds crocodiles
dinosaurs
feathersFeathers are derived character state for birds
characters:
snakes lizards dinosaurs crocodiles
leglessness
Primitive character state is to have legs
Leglessness is a derived character state for snakes
primitive vs. derived characters:unique derived (one clade)shared derived (two or more clades)
primitive vs. derived characters:shared primitive
shared-primitive for this clade
primitive vs. derived characters:
shared-primitive for this clade
shared-derived for this clade
primitive vs. derived characters:shared primitive characters are not useful in
diagnosing a monophyletic group
primitive vs. derived characters:Unique derived characters are not useful in
diagnosing a monophyletic group
primitive vs. derived characters:Only shared derived characters can be used to
diagnose a monophyletic group.
primitive vs. derived characters:Only shared derived characters can be used to
diagnose a monophyletic group.
Correct
Incorrect
Outgroupsused to polarize primitive derived direction
of character state changes in the ingroup
Fig. 11.5
ABCDEO
outgroup
Reconstructing trees1.Choose the taxa
ex: Vertebrates
Reconstructing trees2. Determine the characters
Reconstructing trees3. Determine polarity of characters
Reconstructing trees4. Group taxa by shared derived characters
Reconstructing trees5. Repeat with all characters
work out conflicts (none in this example)
Reconstructing trees6. Complete the tree
Reconstructing trees6. Use parsimony principle to choose the best tree
one change better (shorter tree) than two
Outgroup Species A Species B
Species C Species D Species E
EXCERCISE
Data MatrixCharacter OG Sp A Sp B Sp C Sp D Sp E
Claws 0 1 1 1 0 1
Chin Hair 0 1 1 1 0 1
Horn 0 0 0 1 0 1
Tail 0 1 1 1 1 1
Spikes 0 0 0 1 0 0
Digits 0 0 0 1 0 0
Spots 0 0 0 0 1 0
Tympanum 1 0 0 1 1 1
Lateral Fold 0 1 1 0 1 1
Nostril 1 1 0 1 1 1
Data MatrixCharacter OG Sp A Sp B Sp C Sp D Sp E
Claws 0 1 1 1 0 1
Chin Hair 0 1 1 1 0 1
Horn 0 0 0 1 0 1
Tail 0 1 1 1 1 1
Spikes 0 0 0 1 0 0
Digits 0 0 0 1 0 0
Spots 0 0 0 0 1 0
Tympanum 1 0 0 1 1 1
Lateral Fold 0 1 1 0 1 1
Nostril 1 1 0 1 1 1
ABCE ABCE CEABCDE C C D AB ABDE
B
Molecular phylogenetics
EXCERCISE#Elephas_maximus_(Asian_elephant)AG-G--CT--TGA-AG--GA-AT-TC--T-TGAG-A-A-CAACAAAGCA--A-TCATTTGA-T-TTA---A-GT--AT-AGATGC-T-CAGTATA-AGA-AA-A-A-CA-AA-G-AGAGAC-ATTC-CATCC-C-A--A---TTCCT-T-TGA-ATGT--GTTTTATG-AG-TT-TAT-CAGTCAG-A-ACA--T—CA-T-AT--C-CTT--C-AACA--AGC-AT-TTTGA---GAAA-GGC-A-GAGACAA-T-G-CAT--TAGATT--TTCTT-A-C---CAAA-TCCTATG-A-T
EXCERCISE
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